This tool is designed to assist researchers in selecting polymorphic markers
for a genome scan of a cross between two strains. It uses the Allele Characterization Project dataset in combination with various genetic and
Radiation Hybrid maps.
Genome Scanner Instructions
Based on the selected Genetic or
RH map, markers that are polymorphic are organized into bins based on the desired
scan resolution. For example, to pick polymorphic markers for a 10cM genome
scan you would select a 10cM bin size and you could then pick one marker from
each 10cM bin and thereby get coverage of the desired chromosome(s) at the desired
resolution.
Basic Steps:
Select the two strains to be crossed
Select a map to base the genome
scan bin interval upon
Select the desired bin size (genome
scan resolution). 10cM works well for scans based on genetic maps, 50cR is
best for scans based on RH maps.
Pick one or more chromosomes to
scan
Leave all other options, click
Generate Genome Scanner Output buton
Explanation of the Output Options
Highlight allele size differences
graphically indicates polymorphic markers with size differences within the
selected size range. This facilitates the selection of markers with suitably
spaced alleles for your specific detection system (gel, capillary, etc.)
Autoselect - turning this feature
on will cause the program to automatically select the first polymorphic marker
in each bin with an allele size difference within the size range.
Only Show Markers in this range
causes the polymorphic markers outside of the size range to be hidden from
view.
Output Content - A Chromosome
Statistics table has been added to show various statistics including the number
of polymorphic markers and the corresponding polymorphism percentage for the
chromosome. This table and the genome scan results can be displayed together
or separately. NB These statistics are unaffected by any settings in the
marker size difference range
Output Format - Output can be
in HTML or CSV (Comma separated values, suitable for import into MS Excel,
etc.)